DS-19 system

traitmech:000444 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 19 locus cataloged as working transcriptional unit PDP4 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (8)

DOI:10.1126/science.adv7924
To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain

DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli.
DOI:10.1126/science.adv7924
We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.

DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
PDP4 NZ_RRVV01000031.1 GCF_003886345.1 - True False False True DefensePredictor hits 628 1611 hypothetical protein WP_000020904.1 10.50465077977841 -3.547151294285235 True False Predicted novel defense gene DS-19

The final Science supplementary Table S6 maps working_id PDP4 to DS_name DS-19, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000031.1 positions 628-1611 with product accession WP_000020904.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 PDP4 24-07-25 24-07-25_PDP1_RED1_PDP4_RED7.png 0 1 1 6.342422680822207 True LB 37

The final Science supplementary Table S7 reports a PDP4 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
PDP4 DS-19 True

The final Science supplementary Table S8 maps PDP4 to replicated display name DS-19.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
PDP4 1.0 327.0 WP_000020904.1 PDDEXK PF18742.6 DpnII-MboI ; REase_DpnII-MboI hhpred_9962440.hhr 2.0 76.0 0.718 2024-07-30 00:00:00 192-194 181.0

The final Science supplementary Table S8 reports a lower-probability PDDEXK HHpred hit for WP_000020904.1 in PDP4.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-19 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems |

The pinned DefenseFinder article registry maps the DS-19 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-19__DS-19 | | DS-19 | Custom | 200 |

The pinned DefenseFinder HMM inventory records DS-19__DS-19 as a custom DS-19 profile.

DS-19 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-19 locus to reduced bacteriophage plaquing without resolving DS-19 component function or molecular output.

NONMECHANISTIC · The graph captures DS-19 as the validated PDP4 transcriptional unit with one product accession, a lower-probability PDDEXK HHpred-domain row, and one DefenseFinder DS-19 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-19 molecular activity, trigger, substrate, complete phage breadth, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-19 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-19/PDP4 locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.
- DOI:10.1126/science.adv7924 To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain DeWeirdt et al. describe the plasmid-based phage challenge used to validate predicted transcriptional units.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx PDP4 NZ_RRVV01000031.1 GCF_003886345.1 - True False False True DefensePredictor hits 628 1611 hypothetical protein WP_000020904.1 10.50465077977841 -3.547151294285235 True False Predicted novel defense gene DS-19 The final Science supplementary Table S6 maps working_id PDP4 to DS_name DS-19, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000031.1 positions 628-1611 with product accession WP_000020904.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 PDP4 24-07-25 24-07-25_PDP1_RED1_PDP4_RED7.png 0 1 1 6.342422680822207 True LB 37 The final Science supplementary Table S7 reports a PDP4 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx PDP4 DS-19 True The final Science supplementary Table S8 maps PDP4 to replicated display name DS-19.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-19__DS-19 | | DS-19 | Custom | 200 | The pinned DefenseFinder HMM inventory records DS-19__DS-19 as a custom DS-19 profile.
reduced bacteriophage plaquing confers DS-19 system METPO:2007700
DS-19-mediated phage plaquing reduction realizes the DS-19 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx PDP4 NZ_RRVV01000031.1 GCF_003886345.1 - True False False True DefensePredictor hits 628 1611 hypothetical protein WP_000020904.1 10.50465077977841 -3.547151294285235 True False Predicted novel defense gene DS-19 The final Science supplementary Table S6 maps working_id PDP4 to DS_name DS-19, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000031.1 positions 628-1611 with product accession WP_000020904.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 PDP4 24-07-25 24-07-25_PDP1_RED1_PDP4_RED7.png 0 1 1 6.342422680822207 True LB 37 The final Science supplementary Table S7 reports a PDP4 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342.
- DOI:10.1126/science.adv7924 We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8. The DS nomenclature is used for DefensePredictor discovered systems.
DS-19 system is a phage defense system rdfs:subClassOf
DS-19 system possession is a phage-defense-system trait.
- DOI:10.1126/science.adv7924 We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8. DeWeirdt et al. name validated TUs as DefensePredictor discovered systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | DS-19 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | The pinned DefenseFinder article registry maps the DS-19 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1126/science.adv7924

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

DS-19 EXACT_SYNONYM · DOI:10.1126/science.adv7924
PDP4 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-19__DS-19 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve DS-19 native host breadth, exact profile-to-protein mapping, low-confidence HHpred-domain interpretation, component chemistry, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-19 mechanism children.

KNOWLEDGE GAP OPEN ds-19-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_19_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-19 as the defensive PDP4 transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_000020904.1, a Bas19 phage readout, display name DS-19, and a lower-probability PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-19 custom profile row. The pinned rules table has no DS-19 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK nuclease activity, molecular output, or endogenous DS-19 activity.

Evidence

DOI:10.1126/science.adv7924
We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
PDP4 NZ_RRVV01000031.1 GCF_003886345.1 - True False False True DefensePredictor hits 628 1611 hypothetical protein WP_000020904.1 10.50465077977841 -3.547151294285235 True False Predicted novel defense gene DS-19
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 PDP4 24-07-25 24-07-25_PDP1_RED1_PDP4_RED7.png 0 1 1 6.342422680822207 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
PDP4 DS-19 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
PDP4 1.0 327.0 WP_000020904.1 PDDEXK PF18742.6 DpnII-MboI ; REase_DpnII-MboI hhpred_9962440.hhr 2.0 76.0 0.718 2024-07-30 00:00:00 192-194 181.0
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-19 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-19__DS-19 | | DS-19 | Custom | 200 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-28T21:10:00Z · MINTED_TRAITMECH_ID · codex
Minted DS-19 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at PDP4 transcriptional-unit level because PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v321 reserves the replacement placeholder.
2026-09-28T21:10:01Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-19 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned PDP4 assays in E. coli MG1655 and a DefenseFinder DS-19 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-19 activity. No paid research was used.